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Sample summary
Input data: infant stools
- n samples = 341
- n features: 456
- mean read count: 10^{6}, s.d. = 0
Alpha diversity
Column
Seroconversion
Blue = seroconversion+, Orange = seroconversion-.
Seroconverion - N by country
IND IND (neo+) IND (neo-) MLW
0 204 104 99 46
1 78 45 33 10Mean + s.d.
seroconv Observed.mean Observed.sd Observed.country
1 0 323.18 47.07 IND
2 1 305.42 61.1 IND
3 0 328.99 40.14 IND (neo+)
4 1 308.36 56.64 IND (neo+)
5 0 316.78 53.01 IND (neo-)
6 1 301.42 67.4 IND (neo-)
7 0 317.11 40.72 MLW
8 1 301.5 58.58 MLWSeroconverion - P values
[,1]
IND 0.027523
MLW 0.653142
IND_exposed 0.002213
IND_nonexposed 0.197939RV-IgA
Correlation heatmap
Collated results
rho p n
IND -0.0112 0.851773 282
IND (neo+) -0.0272 0.741617 149
IND (neo-) -0.0598 0.495785 132
MLW -0.2073 0.125205 56Dose 1 shedding
Blue = shed+, Orange = shed-.
Dose 1 shedding - N by country
IND IND (neo+) IND (neo-) MLW
0 207 122 83 26
1 74 25 49 21Mean + s.d.
dose1_shedding Observed.mean Observed.sd Observed.country
1 0 319.79 50.13 IND
2 1 315.45 55.38 IND
3 0 323.03 46.78 IND (neo+)
4 1 325.72 41.97 IND (neo+)
5 0 314.55 55.03 IND (neo-)
6 1 310.2 60.83 IND (neo-)
7 0 318.77 38.86 MLW
8 1 312.86 48.68 MLWDose 1 shedding - P values
[,1]
IND 0.509727
MLW 0.780804
IND_exposed 0.830082
IND_nonexposed 0.431408Beta diversity
Column
Seroconversion
Summary
R2 p n country full outcome
IND_BS3 1.703752 0.015 282 IND 1 seroconversion
INDexp_BS3 2.970485 0.022 149 IND (neo+) 0 seroconversion
INDunexp_BS3 1.193736 0.186 132 IND (neo-) 0 seroconversion
MLW_BS3 1.913009 0.330 56 MLW 1 seroconversionSummary plot
RV-IgA
Summary
R2 p n country full outcome
IND_BS3 0.08365938 0.853 282 IND 1 RV-IgA (post-ORV)
INDexp_BS3 0.33264910 0.603 149 IND (neo+) 0 RV-IgA (post-ORV)
INDunexp_BS3 1.77923614 0.083 132 IND (neo-) 0 RV-IgA (post-ORV)
MLW_BS3 3.73440531 0.107 56 MLW 1 RV-IgA (post-ORV)Summary plot
Dose 1 shedding
Summary
R2 p n country full outcome
IND_BS3 0.16773606 0.594 281 IND 1 dose 1 shedding
INDexp_BS3 0.09027935 0.971 147 IND (neo+) 0 dose 1 shedding
INDunexp_BS3 0.24647872 0.720 132 IND (neo-) 0 dose 1 shedding
MLW_BS3 0.90082949 0.766 47 MLW 1 dose 1 sheddingSummary plot
Random Forests/MaAsLin2
Column
Seroconversion
Summary plot
Differential features - FDR p <0.2
country n_tested_fisher n_signif_fisher n_tested_lr n_signif_lr
1 MLW 246 0 246 0
2 IND (neo-) 272 0 272 0
3 IND (neo+) 247 0 247 0
4 IND 261 94 261 118
n_tested_maaslin n_signif_maaslin
1 397 0
2 404 0
3 402 107
4 401 0
Summary of prevalence difference distribution
Proportion of features more prevalent in non-responders vs responders
country n_neg n_equal n_pos total proportion_neg
1 IND 243 0 18 261 93.1%
2 IND (neo+) 222 0 25 247 89.9%
3 IND (neo-) 231 8 33 272 84.9%
4 MLW 191 0 55 246 77.6%n = prevalence difference <0 (vs >=0).
P values (Wilcoxon test, mean of difference distribution = 0)
[,1]
IND 3.796283e-41
MLW 6.137398e-18
IND_exposed 1.598258e-37
IND_nonexposed 2.386535e-30Summary of adundance difference distribution
P values (Wilcoxon test, mean of difference distribution = 0)
[,1]
IND 3.750220e-23
MLW 8.508526e-16
IND_exposed 1.631855e-25
IND_nonexposed 9.264123e-14Proportion of features more abundant in non-responders vs responders
country n_neg n_equal n_pos total proportion_neg
1 IND 297 0 104 401 74.1%
2 IND (neo+) 287 0 115 402 71.4%
3 IND (neo-) 275 0 129 404 68.1%
4 MLW 286 0 111 397 72%Summary of MaAsLin2 associations
subset N_features FDR p<0.2 unadjusted FDR p<0.2 adjusted
1 IND 401 (104 +/297 -) 171 (30 +/141 -) 0 (0 +/0 -)
2 IND (neo+) 402 (115 +/287 -) 155 (11 +/144 -) 107 (3 +/104 -)
3 IND (neo-) 404 (129 +/275 -) 0 (0 +/0 -) 0 (0 +/0 -)
4 MLW 397 (111 +/286 -) 0 (0 +/0 -) 0 (0 +/0 -)Spearman’s rho matrix of statistical test p values - India
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.0000000 0.9942945 0.9764945 0.7086440
LR p 0.9942945 1.0000000 0.9826503 0.7065510
LR (adj) p 0.9764945 0.9826503 1.0000000 0.7024705
Wilcox p 0.7086440 0.7065510 0.7024705 1.0000000
Maaslin p 0.6723723 0.6789342 0.6799156 0.9302881
Maaslin (adj) p 0.6278578 0.6339029 0.6515367 0.9117784
RF rank 0.1224476 0.1189391 0.1088023 0.2229810
Inv. abs. Maaslin coef. (adj) 0.5236653 0.5387589 0.5593848 0.7909744
Inv. abs. Prev. diff. 0.8883787 0.8908380 0.8479131 0.5781416
Inv. abs. ean abund. diff. 0.3832242 0.3984043 0.4126446 0.6372368
Maaslin p Maaslin (adj) p RF rank
Fisher p 0.6723723 0.6278578 0.1224476
LR p 0.6789342 0.6339029 0.1189391
LR (adj) p 0.6799156 0.6515367 0.1088023
Wilcox p 0.9302881 0.9117784 0.2229810
Maaslin p 1.0000000 0.9739168 0.2748655
Maaslin (adj) p 0.9739168 1.0000000 0.2847501
RF rank 0.2748655 0.2847501 1.0000000
Inv. abs. Maaslin coef. (adj) 0.8447937 0.8466060 0.3893987
Inv. abs. Prev. diff. 0.5325539 0.4710106 0.1052585
Inv. abs. ean abund. diff. 0.7154635 0.6909805 0.3773935
Inv. abs. Maaslin coef. (adj)
Fisher p 0.5236653
LR p 0.5387589
LR (adj) p 0.5593848
Wilcox p 0.7909744
Maaslin p 0.8447937
Maaslin (adj) p 0.8466060
RF rank 0.3893987
Inv. abs. Maaslin coef. (adj) 1.0000000
Inv. abs. Prev. diff. 0.3370054
Inv. abs. ean abund. diff. 0.9359808
Inv. abs. Prev. diff. Inv. abs. ean abund. diff.
Fisher p 0.8883787 0.3832242
LR p 0.8908380 0.3984043
LR (adj) p 0.8479131 0.4126446
Wilcox p 0.5781416 0.6372368
Maaslin p 0.5325539 0.7154635
Maaslin (adj) p 0.4710106 0.6909805
RF rank 0.1052585 0.3773935
Inv. abs. Maaslin coef. (adj) 0.3370054 0.9359808
Inv. abs. Prev. diff. 1.0000000 0.2002457
Inv. abs. ean abund. diff. 0.2002457 1.0000000
N features with full data across tests: 261
Spearman’s rho matrix of statistical test p values - India (neo+)
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.0000000 0.9622760 0.9306486 0.7447968
LR p 0.9622760 1.0000000 0.9700610 0.7316161
LR (adj) p 0.9306486 0.9700610 1.0000000 0.7223993
Wilcox p 0.7447968 0.7316161 0.7223993 1.0000000
Maaslin p 0.6885704 0.6930007 0.6877306 0.9430069
Maaslin (adj) p 0.6386859 0.6566272 0.6704401 0.9175299
RF rank 0.2486502 0.2693089 0.2928691 0.3237608
Inv. abs. Maaslin coef. (adj) 0.6039889 0.6233117 0.6180852 0.8425036
Inv. abs. prev. diff. 0.8759253 0.8748381 0.8614434 0.5702970
Inv. abs. mean abund. diff. 0.5180994 0.5330874 0.5166509 0.7433007
Maaslin p Maaslin (adj) p RF rank
Fisher p 0.6885704 0.6386859 0.2486502
LR p 0.6930007 0.6566272 0.2693089
LR (adj) p 0.6877306 0.6704401 0.2928691
Wilcox p 0.9430069 0.9175299 0.3237608
Maaslin p 1.0000000 0.9649012 0.3568645
Maaslin (adj) p 0.9649012 1.0000000 0.3703465
RF rank 0.3568645 0.3703465 1.0000000
Inv. abs. Maaslin coef. (adj) 0.8755467 0.9075972 0.3633562
Inv. abs. prev. diff. 0.4982767 0.4398010 0.2680478
Inv. abs. mean abund. diff. 0.7799912 0.7864455 0.3019440
Inv. abs. Maaslin coef. (adj)
Fisher p 0.6039889
LR p 0.6233117
LR (adj) p 0.6180852
Wilcox p 0.8425036
Maaslin p 0.8755467
Maaslin (adj) p 0.9075972
RF rank 0.3633562
Inv. abs. Maaslin coef. (adj) 1.0000000
Inv. abs. prev. diff. 0.3769586
Inv. abs. mean abund. diff. 0.9481350
Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p 0.8759253 0.5180994
LR p 0.8748381 0.5330874
LR (adj) p 0.8614434 0.5166509
Wilcox p 0.5702970 0.7433007
Maaslin p 0.4982767 0.7799912
Maaslin (adj) p 0.4398010 0.7864455
RF rank 0.2680478 0.3019440
Inv. abs. Maaslin coef. (adj) 0.3769586 0.9481350
Inv. abs. prev. diff. 1.0000000 0.2887131
Inv. abs. mean abund. diff. 0.2887131 1.0000000
N features with full data across tests: 247
Spearman’s rho matrix of statistical test p values - India (neo-)
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.0000000 0.8841897 0.7801207 0.50155041
LR p 0.8841897 1.0000000 0.8912043 0.39633764
LR (adj) p 0.7801207 0.8912043 1.0000000 0.23592209
Wilcox p 0.5015504 0.3963376 0.2359221 1.00000000
Maaslin p 0.4695774 0.3556114 0.2446995 0.84144414
Maaslin (adj) p 0.5101192 0.3880124 0.3229939 0.82149917
RF rank 0.2105918 0.2888273 0.2637084 0.02446357
Inv. abs. Maaslin coef. (adj) 0.3779023 0.4139385 0.4889670 0.51832327
Inv. abs. prev. diff. 0.8767241 0.8562316 0.7206986 0.49543130
Inv. abs. mean abund. diff. 0.1571692 0.2147318 0.2889432 0.28404164
Maaslin p Maaslin (adj) p RF rank
Fisher p 0.46957738 0.51011923 0.21059177
LR p 0.35561145 0.38801238 0.28882730
LR (adj) p 0.24469953 0.32299389 0.26370841
Wilcox p 0.84144414 0.82149917 0.02446357
Maaslin p 1.00000000 0.92573857 0.06794382
Maaslin (adj) p 0.92573857 1.00000000 0.07367448
RF rank 0.06794382 0.07367448 1.00000000
Inv. abs. Maaslin coef. (adj) 0.62959807 0.73203343 0.26472436
Inv. abs. prev. diff. 0.37958937 0.40808420 0.16817176
Inv. abs. mean abund. diff. 0.39964894 0.38685958 0.45166737
Inv. abs. Maaslin coef. (adj)
Fisher p 0.3779023
LR p 0.4139385
LR (adj) p 0.4889670
Wilcox p 0.5183233
Maaslin p 0.6295981
Maaslin (adj) p 0.7320334
RF rank 0.2647244
Inv. abs. Maaslin coef. (adj) 1.0000000
Inv. abs. prev. diff. 0.2508487
Inv. abs. mean abund. diff. 0.7021987
Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p 0.87672415 0.15716918
LR p 0.85623159 0.21473183
LR (adj) p 0.72069860 0.28894323
Wilcox p 0.49543130 0.28404164
Maaslin p 0.37958937 0.39964894
Maaslin (adj) p 0.40808420 0.38685958
RF rank 0.16817176 0.45166737
Inv. abs. Maaslin coef. (adj) 0.25084874 0.70219874
Inv. abs. prev. diff. 1.00000000 0.03499244
Inv. abs. mean abund. diff. 0.03499244 1.00000000
N features with full data across tests: 272
Spearman’s rho matrix of statistical test p values - Malawi
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.00000000 0.6506564 0.5839612 0.367315701
LR p 0.65065635 1.0000000 0.9206689 0.290664870
LR (adj) p 0.58396122 0.9206689 1.0000000 0.225117860
Wilcox p 0.36731570 0.2906649 0.2251179 1.000000000
Maaslin p 0.40346321 0.2375814 0.1852654 0.741420119
Maaslin (adj) p 0.43334091 0.2445501 0.2218286 0.673152685
RF rank 0.04693842 0.1055699 0.1523625 0.003072444
Inv. abs. maaslin coef. (adj) 0.52524974 0.3596353 0.3590754 0.408958919
Inv. abs. prev. diff. 0.73451218 0.6761914 0.5986336 0.493536121
Inv. abs. mean abund. diff. 0.36038518 0.2856644 0.2800041 0.289432366
Maaslin p Maaslin (adj) p RF rank
Fisher p 0.40346321 0.43334091 0.046938418
LR p 0.23758144 0.24455007 0.105569859
LR (adj) p 0.18526537 0.22182855 0.152362538
Wilcox p 0.74142012 0.67315268 0.003072444
Maaslin p 1.00000000 0.92485761 0.010914071
Maaslin (adj) p 0.92485761 1.00000000 0.010339328
RF rank 0.01091407 0.01033933 1.000000000
Inv. abs. maaslin coef. (adj) 0.65509614 0.76554702 0.310460766
Inv. abs. prev. diff. 0.42495186 0.37418793 -0.031603542
Inv. abs. mean abund. diff. 0.42746835 0.44278009 0.456813062
Inv. abs. maaslin coef. (adj)
Fisher p 0.5252497
LR p 0.3596353
LR (adj) p 0.3590754
Wilcox p 0.4089589
Maaslin p 0.6550961
Maaslin (adj) p 0.7655470
RF rank 0.3104608
Inv. abs. maaslin coef. (adj) 1.0000000
Inv. abs. prev. diff. 0.3053149
Inv. abs. mean abund. diff. 0.7807411
Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p 0.73451218 0.3603852
LR p 0.67619139 0.2856644
LR (adj) p 0.59863356 0.2800041
Wilcox p 0.49353612 0.2894324
Maaslin p 0.42495186 0.4274683
Maaslin (adj) p 0.37418793 0.4427801
RF rank -0.03160354 0.4568131
Inv. abs. maaslin coef. (adj) 0.30531489 0.7807411
Inv. abs. prev. diff. 1.00000000 0.1747271
Inv. abs. mean abund. diff. 0.17472709 1.0000000
N features with full data across tests: 246
RV-IgA
Summary plot
Differential features - p <0.2
country n_tested_wilcox n_signif_wilcox n_tested_lr n_signif_lr
1 MLW 223 0 223 0
2 IND (neo-) 247 0 247 127
3 IND (neo+) 225 0 225 0
4 IND 238 0 238 0
n_tested_maaslin n_signif_maaslin
1 392 0
2 396 0
3 399 0
4 395 0
Summary of GMRs
Proportion of features negatively vs positively correlated with RV-IgA
country n_neg n_equal n_pos total proportion_neg
1 IND 98 0 140 238 41.2%
2 IND (neo+) 73 0 152 225 32.4%
3 IND (neo-) 215 0 32 247 87%
4 MLW 193 0 30 223 86.5%n = GM ratio <1 (vs >=1).
P values (Wilcoxon test, mean of difference distribution = 1)
[,1]
IND 6.969405e-03
MLW 1.075839e-26
IND_exposed 1.115465e-09
IND_nonexposed 7.492957e-30Summary of adundance difference distribution
P values (Wilcoxon test, mean of difference distribution = 0)
[,1]
IND 2.524401e-01
MLW 7.619771e-12
IND_exposed 9.999319e-08
IND_nonexposed 3.182365e-18Proportion of features negatively vs positively correlated with RV-IgA
country n_neg n_equal n_pos total proportion_neg
1 IND 170 0 225 395 43%
2 IND (neo+) 141 0 258 399 35.3%
3 IND (neo-) 283 0 113 396 71.5%
4 MLW 250 0 142 392 63.8%Summary of MaAsLin2 associations
subset N_features FDR p<0.2 unadjusted FDR p<0.2 adjusted
1 IND 395 (225 +/170 -) 0 (0 +/0 -) 0 (0 +/0 -)
2 IND (neo+) 399 (258 +/141 -) 0 (0 +/0 -) 0 (0 +/0 -)
3 IND (neo-) 396 (113 +/283 -) 0 (0 +/0 -) 0 (0 +/0 -)
4 MLW 392 (142 +/250 -) 0 (0 +/0 -) 0 (0 +/0 -)Spearman’s rho matrix of statistical test p values - India
#### Rho values
Spearman p LR p LR (adj) p Wilcox p
Spearman p 1.000000000 0.019787610 -0.02419742 0.39966486
LR p 0.019787610 1.000000000 0.89923771 -0.09265696
LR (adj) p -0.024197418 0.899237713 1.00000000 -0.16190588
Wilcox p 0.399664858 -0.092656956 -0.16190588 1.00000000
Maaslin p 0.847769132 -0.024872147 -0.02537152 0.24696297
Maaslin (adj) p 0.401495442 -0.046553548 0.04285853 0.18062093
RF rank 0.005821973 0.006003607 -0.01766900 -0.12078470
Inv. abs. maaslin coef. (adj) 0.284134407 0.026875876 0.09585544 0.04410029
Inv. abs. GMR-1 0.334829825 0.063930678 -0.04509138 0.89951722
Maaslin p Maaslin (adj) p RF rank
Spearman p 0.84776913 0.40149544 0.005821973
LR p -0.02487215 -0.04655355 0.006003607
LR (adj) p -0.02537152 0.04285853 -0.017669004
Wilcox p 0.24696297 0.18062093 -0.120784702
Maaslin p 1.00000000 0.53072509 -0.039048287
Maaslin (adj) p 0.53072509 1.00000000 -0.099249455
RF rank -0.03904829 -0.09924945 1.000000000
Inv. abs. maaslin coef. (adj) 0.40162932 0.84203775 0.169519014
Inv. abs. GMR-1 0.14697501 0.08235363 -0.019484016
Inv. abs. maaslin coef. (adj) Inv. abs. GMR-1
Spearman p 0.28413441 0.33482983
LR p 0.02687588 0.06393068
LR (adj) p 0.09585544 -0.04509138
Wilcox p 0.04410029 0.89951722
Maaslin p 0.40162932 0.14697501
Maaslin (adj) p 0.84203775 0.08235363
RF rank 0.16951901 -0.01948402
Inv. abs. maaslin coef. (adj) 1.00000000 0.02222840
Inv. abs. GMR-1 0.02222840 1.00000000
N features with full data across tests: 238
Spearman’s rho matrix of statistical test p values - India (neo+)
#### Rho values
Spearman p LR p LR (adj) p Wilcox p
Spearman p 1.00000000 0.23858536 0.054319220 0.416849259
LR p 0.23858536 1.00000000 0.745480731 0.379558287
LR (adj) p 0.05431922 0.74548073 1.000000000 0.236372319
Wilcox p 0.41684926 0.37955829 0.236372319 1.000000000
Maaslin p 0.75540386 0.12380156 0.000917111 0.270599062
Maaslin (adj) p 0.17531975 0.02235623 0.031593711 0.150312561
RF rank 0.17247105 0.18119132 0.119449545 0.019593264
Inv. abs. maaslin coef. (adj) 0.06787125 0.07136293 0.056649121 0.001095161
Inv. abs. GMR-1 0.33811380 0.40535295 0.218477851 0.846347115
Maaslin p Maaslin (adj) p RF rank
Spearman p 0.755403860 0.17531975 0.17247105
LR p 0.123801560 0.02235623 0.18119132
LR (adj) p 0.000917111 0.03159371 0.11944955
Wilcox p 0.270599062 0.15031256 0.01959326
Maaslin p 1.000000000 0.26548668 0.04991639
Maaslin (adj) p 0.265486684 1.00000000 0.01458864
RF rank 0.049916390 0.01458864 1.00000000
Inv. abs. maaslin coef. (adj) 0.052032012 0.81115672 0.23694074
Inv. abs. GMR-1 0.140044065 -0.07835215 0.07778406
Inv. abs. maaslin coef. (adj) Inv. abs. GMR-1
Spearman p 0.067871250 0.33811380
LR p 0.071362932 0.40535295
LR (adj) p 0.056649121 0.21847785
Wilcox p 0.001095161 0.84634711
Maaslin p 0.052032012 0.14004406
Maaslin (adj) p 0.811156723 -0.07835215
RF rank 0.236940741 0.07778406
Inv. abs. maaslin coef. (adj) 1.000000000 -0.09837372
Inv. abs. GMR-1 -0.098373721 1.00000000
N features with full data across tests: 225
Spearman’s rho matrix of statistical test p values - India (neo-)
#### Rho values
Spearman p LR p LR (adj) p Wilcox p
Spearman p 1.00000000 -0.04965554 -0.1411532 0.4640689
LR p -0.04965554 1.00000000 0.9445954 0.5774813
LR (adj) p -0.14115316 0.94459536 1.0000000 0.5034800
Wilcox p 0.46406892 0.57748128 0.5034800 1.0000000
Maaslin p 0.63264575 0.29591165 0.2140919 0.4869308
Maaslin (adj) p 0.54457832 0.42212336 0.3724083 0.5441302
RF rank 0.26917965 0.13232699 0.1117772 0.2419813
Inv. abs. maaslin coef. (adj) 0.18085479 0.47363916 0.4992769 0.3273054
Inv. abs. GMR-1 0.22976497 0.71190313 0.6566444 0.8626317
Maaslin p Maaslin (adj) p RF rank
Spearman p 0.6326458 0.5445783 0.2691797
LR p 0.2959116 0.4221234 0.1323270
LR (adj) p 0.2140919 0.3724083 0.1117772
Wilcox p 0.4869308 0.5441302 0.2419813
Maaslin p 1.0000000 0.9031593 0.1959402
Maaslin (adj) p 0.9031593 1.0000000 0.1957571
RF rank 0.1959402 0.1957571 1.0000000
Inv. abs. maaslin coef. (adj) 0.6394014 0.7829229 0.1457127
Inv. abs. GMR-1 0.4817301 0.5532486 0.2246642
Inv. abs. maaslin coef. (adj) Inv. abs. GMR-1
Spearman p 0.1808548 0.2297650
LR p 0.4736392 0.7119031
LR (adj) p 0.4992769 0.6566444
Wilcox p 0.3273054 0.8626317
Maaslin p 0.6394014 0.4817301
Maaslin (adj) p 0.7829229 0.5532486
RF rank 0.1457127 0.2246642
Inv. abs. maaslin coef. (adj) 1.0000000 0.4709555
Inv. abs. GMR-1 0.4709555 1.0000000
N features with full data across tests: 247
Spearman’s rho matrix of statistical test p values - Malawi
#### Rho values
Spearman p LR p LR (adj) p Wilcox p
Spearman p 1.00000000 0.2922950 0.18405522 0.51556652
LR p 0.29229502 1.0000000 0.80226678 0.54373426
LR (adj) p 0.18405522 0.8022668 1.00000000 0.56290132
Wilcox p 0.51556652 0.5437343 0.56290132 1.00000000
Maaslin p 0.55791072 0.3459296 0.23484449 0.43400812
Maaslin (adj) p 0.54818347 0.3161935 0.24468451 0.41689443
RF rank 0.08360109 -0.1051776 0.02280431 0.07500572
Inv. abs. maaslin coef. (adj) 0.44003135 0.2384487 0.25149379 0.39074745
Inv. abs. GMR-1 0.32388062 0.4482257 0.64149501 0.77959456
Maaslin p Maaslin (adj) p RF rank
Spearman p 0.5579107 0.5481835 0.08360109
LR p 0.3459296 0.3161935 -0.10517763
LR (adj) p 0.2348445 0.2446845 0.02280431
Wilcox p 0.4340081 0.4168944 0.07500572
Maaslin p 1.0000000 0.9263634 0.17186338
Maaslin (adj) p 0.9263634 1.0000000 0.16488477
RF rank 0.1718634 0.1648848 1.00000000
Inv. abs. maaslin coef. (adj) 0.7613034 0.8692585 0.20483027
Inv. abs. GMR-1 0.2072013 0.2154002 0.18061766
Inv. abs. maaslin coef. (adj) Inv. abs. GMR-1
Spearman p 0.4400313 0.3238806
LR p 0.2384487 0.4482257
LR (adj) p 0.2514938 0.6414950
Wilcox p 0.3907475 0.7795946
Maaslin p 0.7613034 0.2072013
Maaslin (adj) p 0.8692585 0.2154002
RF rank 0.2048303 0.1806177
Inv. abs. maaslin coef. (adj) 1.0000000 0.2598658
Inv. abs. GMR-1 0.2598658 1.0000000
N features with full data across tests: 223
Dose 1 shedding
Summary plot
Differential features - FDR p <0.2
country n_tested_fisher n_signif_fisher n_tested_lr n_signif_lr
1 MLW 226 0 226 0
2 IND (neo-) 263 0 263 0
3 IND (neo+) 235 0 235 0
4 IND 262 0 262 0
n_tested_maaslin n_signif_maaslin
1 399 0
2 398 0
3 405 0
4 403 0
Summary of prevalence difference distribution
Proportion of features more prevalent in non-responders vs responders
country n_neg n_equal n_pos total proportion_neg
1 IND 170 8 84 262 64.9%
2 IND (neo+) 90 0 145 235 38.3%
3 IND (neo-) 160 0 103 263 60.8%
4 MLW 147 0 79 226 65%n = prevalence difference <0 (vs >=0).
P values (Wilcoxon test, mean of difference distribution = 0)
[,1]
IND 3.529274e-10
MLW 1.678144e-05
IND_exposed 4.044205e-04
IND_nonexposed 2.465230e-06Summary of adundance difference distribution
P values (Wilcoxon test, mean of difference distribution = 0)
[,1]
IND 2.208431e-13
MLW 2.913547e-15
IND_exposed 1.836801e-04
IND_nonexposed 1.703317e-05Proportion of features more abundant in non-responders vs responders
country n_neg n_equal n_pos total proportion_neg
1 IND 260 0 143 403 64.5%
2 IND (neo+) 238 0 167 405 58.8%
3 IND (neo-) 222 0 176 398 55.8%
4 MLW 141 0 258 399 35.3%Summary of MaAsLin2 associations
subset N_features FDR p<0.2 unadjusted FDR p<0.2 adjusted
1 IND 403 (143 +/260 -) 0 (0 +/0 -) 0 (0 +/0 -)
2 IND (neo+) 405 (167 +/238 -) 0 (0 +/0 -) 0 (0 +/0 -)
3 IND (neo-) 398 (176 +/222 -) 0 (0 +/0 -) 0 (0 +/0 -)
4 MLW 399 (258 +/141 -) 0 (0 +/0 -) 0 (0 +/0 -)Spearman’s rho matrix of statistical test p values - India
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.000000000 0.974335245 0.94231801 0.572664200
LR p 0.974335245 1.000000000 0.95808536 0.576054827
LR (adj) p 0.942318007 0.958085357 1.00000000 0.568493906
Wilcox p 0.572664200 0.576054827 0.56849391 1.000000000
Maaslin p 0.406539385 0.410949019 0.40568358 0.760741784
Maaslin (adj) p 0.450558782 0.452902208 0.46857231 0.681881654
RF rank 0.146223308 0.121939152 0.13451846 0.004478544
Inv. abs. Maaslin coef. (adj) 0.327349151 0.320335081 0.34987304 0.598119934
Inv. abs. prev. diff. 0.928700379 0.949638568 0.90770566 0.541926066
Inv. abs. mean abund. diff. 0.009019307 -0.003693245 0.03338857 0.275925549
Maaslin p Maaslin (adj) p RF rank
Fisher p 0.406539385 0.45055878 0.146223308
LR p 0.410949019 0.45290221 0.121939152
LR (adj) p 0.405683577 0.46857231 0.134518457
Wilcox p 0.760741784 0.68188165 0.004478544
Maaslin p 1.000000000 0.87031810 0.007925193
Maaslin (adj) p 0.870318103 1.00000000 0.063562013
RF rank 0.007925193 0.06356201 1.000000000
Inv. abs. Maaslin coef. (adj) 0.653706751 0.73682423 0.379928495
Inv. abs. prev. diff. 0.386667261 0.48007388 0.173088996
Inv. abs. mean abund. diff. 0.221809197 0.04118508 0.218031039
Inv. abs. Maaslin coef. (adj)
Fisher p 0.3273492
LR p 0.3203351
LR (adj) p 0.3498730
Wilcox p 0.5981199
Maaslin p 0.6537068
Maaslin (adj) p 0.7368242
RF rank 0.3799285
Inv. abs. Maaslin coef. (adj) 1.0000000
Inv. abs. prev. diff. 0.3322935
Inv. abs. mean abund. diff. 0.5443872
Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p 0.9287004 0.009019307
LR p 0.9496386 -0.003693245
LR (adj) p 0.9077057 0.033388571
Wilcox p 0.5419261 0.275925549
Maaslin p 0.3866673 0.221809197
Maaslin (adj) p 0.4800739 0.041185082
RF rank 0.1730890 0.218031039
Inv. abs. Maaslin coef. (adj) 0.3322935 0.544387195
Inv. abs. prev. diff. 1.0000000 -0.103914787
Inv. abs. mean abund. diff. -0.1039148 1.000000000
N features with full data across tests: 262
Spearman’s rho matrix of statistical test p values - India (neo+)
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.00000000 0.74220478 0.68723864 0.41585075
LR p 0.74220478 1.00000000 0.77664271 0.31558977
LR (adj) p 0.68723864 0.77664271 1.00000000 0.28689611
Wilcox p 0.41585075 0.31558977 0.28689611 1.00000000
Maaslin p 0.26489041 0.11454713 0.16691425 0.74747922
Maaslin (adj) p 0.26769444 0.13149647 0.23384621 0.45368235
RF rank -0.03708142 0.02400939 -0.02591442 -0.03022754
Inv. abs. Maaslin coef. (adj) 0.07393640 0.01062299 0.11313002 0.37492134
Inv. abs. prev. diff. 0.85539687 0.80584358 0.62032202 0.31486252
Inv. abs. mean abund. diff. -0.10748088 -0.09311852 -0.07531290 0.30928563
Maaslin p Maaslin (adj) p RF rank
Fisher p 0.26489041 0.26769444 -0.037081425
LR p 0.11454713 0.13149647 0.024009391
LR (adj) p 0.16691425 0.23384621 -0.025914420
Wilcox p 0.74747922 0.45368235 -0.030227536
Maaslin p 1.00000000 0.58043930 -0.044919529
Maaslin (adj) p 0.58043930 1.00000000 -0.018373187
RF rank -0.04491953 -0.01837319 1.000000000
Inv. abs. Maaslin coef. (adj) 0.40317320 0.64561944 0.400068518
Inv. abs. prev. diff. 0.12924106 0.27565921 0.004467213
Inv. abs. mean abund. diff. 0.31183132 -0.14374721 0.397335194
Inv. abs. Maaslin coef. (adj)
Fisher p 0.07393640
LR p 0.01062299
LR (adj) p 0.11313002
Wilcox p 0.37492134
Maaslin p 0.40317320
Maaslin (adj) p 0.64561944
RF rank 0.40006852
Inv. abs. Maaslin coef. (adj) 1.00000000
Inv. abs. prev. diff. 0.04905669
Inv. abs. mean abund. diff. 0.45829845
Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p 0.855396873 -0.10748088
LR p 0.805843583 -0.09311852
LR (adj) p 0.620322018 -0.07531290
Wilcox p 0.314862520 0.30928563
Maaslin p 0.129241063 0.31183132
Maaslin (adj) p 0.275659207 -0.14374721
RF rank 0.004467213 0.39733519
Inv. abs. Maaslin coef. (adj) 0.049056693 0.45829845
Inv. abs. prev. diff. 1.000000000 -0.25815841
Inv. abs. mean abund. diff. -0.258158415 1.00000000
N features with full data across tests: 235
Spearman’s rho matrix of statistical test p values - India (neo-)
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.0000000 0.9172720 0.8342413 0.4500943
LR p 0.9172720 1.0000000 0.8785108 0.4121878
LR (adj) p 0.8342413 0.8785108 1.0000000 0.3149790
Wilcox p 0.4500943 0.4121878 0.3149790 1.0000000
Maaslin p 0.2487006 0.2155935 0.1213636 0.7362519
Maaslin (adj) p 0.2415929 0.2183786 0.1474333 0.7183529
RF rank 0.2479525 0.2483479 0.2616240 0.2354034
Inv. abs. Maaslin coef. (adj) 0.2106117 0.2187138 0.1675265 0.6127869
Inv. abs. prev. diff. 0.9403201 0.9152809 0.8020081 0.4800086
Inv. abs. mean abund. diff. 0.1339443 0.1662158 0.1545637 0.2899922
Maaslin p Maaslin (adj) p RF rank
Fisher p 0.24870062 0.24159295 0.24795253
LR p 0.21559347 0.21837864 0.24834792
LR (adj) p 0.12136356 0.14743334 0.26162400
Wilcox p 0.73625186 0.71835287 0.23540345
Maaslin p 1.00000000 0.90660023 0.08286837
Maaslin (adj) p 0.90660023 1.00000000 0.03612473
RF rank 0.08286837 0.03612473 1.00000000
Inv. abs. Maaslin coef. (adj) 0.74216658 0.77595652 0.33044869
Inv. abs. prev. diff. 0.29942638 0.30742993 0.22344898
Inv. abs. mean abund. diff. 0.31953669 0.22782566 0.46169500
Inv. abs. Maaslin coef. (adj)
Fisher p 0.2106117
LR p 0.2187138
LR (adj) p 0.1675265
Wilcox p 0.6127869
Maaslin p 0.7421666
Maaslin (adj) p 0.7759565
RF rank 0.3304487
Inv. abs. Maaslin coef. (adj) 1.0000000
Inv. abs. prev. diff. 0.2481751
Inv. abs. mean abund. diff. 0.6261568
Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p 0.94032009 0.13394431
LR p 0.91528087 0.16621580
LR (adj) p 0.80200807 0.15456370
Wilcox p 0.48000861 0.28999221
Maaslin p 0.29942638 0.31953669
Maaslin (adj) p 0.30742993 0.22782566
RF rank 0.22344898 0.46169500
Inv. abs. Maaslin coef. (adj) 0.24817513 0.62615684
Inv. abs. prev. diff. 1.00000000 0.09590704
Inv. abs. mean abund. diff. 0.09590704 1.00000000
N features with full data across tests: 263
Spearman’s rho matrix of statistical test p values - Malawi
#### Rho values
Fisher p LR p LR (adj) p Wilcox p
Fisher p 1.00000000 0.58156928 0.41213005 0.4023554
LR p 0.58156928 1.00000000 0.81004406 0.2377641
LR (adj) p 0.41213005 0.81004406 1.00000000 0.2283727
Wilcox p 0.40235539 0.23776409 0.22837268 1.0000000
Maaslin p 0.34695960 0.16677668 0.20966945 0.8167699
Maaslin (adj) p 0.24011916 0.11464428 0.22035436 0.5769154
RF rank 0.02511153 0.13449865 0.15034104 0.1140234
Inv. abs. Maaslin coef. (adj) 0.11066107 0.12708374 0.20557618 0.3477212
Inv. abs. prev. diff. 0.91452665 0.68028410 0.53439862 0.4498594
Inv. abs. mean abund. diff. -0.01614366 0.02294581 0.03544569 0.2385908
Maaslin p Maaslin (adj) p RF rank
Fisher p 0.3469596 0.24011916 0.02511153
LR p 0.1667767 0.11464428 0.13449865
LR (adj) p 0.2096694 0.22035436 0.15034104
Wilcox p 0.8167699 0.57691543 0.11402344
Maaslin p 1.0000000 0.74098730 0.12467389
Maaslin (adj) p 0.7409873 1.00000000 0.08820684
RF rank 0.1246739 0.08820684 1.00000000
Inv. abs. Maaslin coef. (adj) 0.5172681 0.75761885 0.41242445
Inv. abs. prev. diff. 0.3904786 0.27916761 0.05905156
Inv. abs. mean abund. diff. 0.3256891 0.07852582 0.46383574
Inv. abs. Maaslin coef. (adj)
Fisher p 0.1106611
LR p 0.1270837
LR (adj) p 0.2055762
Wilcox p 0.3477212
Maaslin p 0.5172681
Maaslin (adj) p 0.7576189
RF rank 0.4124245
Inv. abs. Maaslin coef. (adj) 1.0000000
Inv. abs. prev. diff. 0.1473162
Inv. abs. mean abund. diff. 0.5077193
Inv. abs. prev. diff. Inv. abs. mean abund. diff.
Fisher p 0.91452665 -0.01614366
LR p 0.68028410 0.02294581
LR (adj) p 0.53439862 0.03544569
Wilcox p 0.44985939 0.23859082
Maaslin p 0.39047857 0.32568914
Maaslin (adj) p 0.27916761 0.07852582
RF rank 0.05905156 0.46383574
Inv. abs. Maaslin coef. (adj) 0.14731624 0.50771931
Inv. abs. prev. diff. 1.00000000 0.02487736
Inv. abs. mean abund. diff. 0.02487736 1.00000000
N features with full data across tests: 226
Summary plots
Seroconversion
IgA
Dose 1 shedding
Session info
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] Maaslin2_1.10.0 FSA_0.9.3 ALDEx2_1.28.1
[4] zCompositions_1.4.0-1 truncnorm_1.0-8 NADA_1.6-1.1
[7] survival_3.4-0 MASS_7.3-58.1 sjstats_0.18.1
[10] ggExtra_0.10.0 formattable_0.2.1 inlmisc_0.5.5
[13] wesanderson_0.3.6 phangorn_2.10.0 ape_5.6-2
[16] DECIPHER_2.24.0 RSQLite_2.2.18 Biostrings_2.64.1
[19] GenomeInfoDb_1.32.4 XVector_0.36.0 IRanges_2.30.1
[22] S4Vectors_0.34.0 BiocGenerics_0.42.0 cowplot_1.1.1
[25] scales_1.2.1 RVAideMemoire_0.9-81-2 DescTools_0.99.47
[28] ggsignif_0.6.4 binom_1.1-1.1 shiny_1.7.3
[31] randomcoloR_1.1.0.1 crossval_1.0.4 labdsv_2.0-1
[34] mgcv_1.8-41 nlme_3.1-160 ggpubr_0.4.0
[37] data.table_1.14.4 corrplot_0.92 vegan_2.6-4
[40] lattice_0.20-45 permute_0.9-7 randomForest_4.7-1.1
[43] matrixStats_0.62.0 lme4_1.1-30 Matrix_1.5-1
[46] reshape2_1.4.4 pheatmap_1.0.12 DT_0.26
[49] plotly_4.10.0 cluster_2.1.4 tidyr_1.2.1
[52] dplyr_1.0.10 magrittr_2.0.3 plyr_1.8.7
[55] kableExtra_1.3.4 gridExtra_2.3 RColorBrewer_1.1-3
[58] knitr_1.40 ggplot2_3.3.6 phyloseq_1.40.0
loaded via a namespace (and not attached):
[1] estimability_1.4.1 coda_0.19-4
[3] bit64_4.0.5 DelayedArray_0.22.0
[5] RCurl_1.98-1.9 generics_0.1.3
[7] terra_1.6-17 proxy_0.4-27
[9] bit_4.0.4 webshot_0.5.4
[11] xml2_1.3.3 httpuv_1.6.6
[13] SummarizedExperiment_1.26.1 assertthat_0.2.1
[15] xfun_0.34 jquerylib_0.1.4
[17] evaluate_0.17 promises_1.2.0.1
[19] DEoptimR_1.0-11 fansi_1.0.3
[21] readxl_1.4.1 igraph_1.3.5
[23] DBI_1.1.3 htmlwidgets_1.5.4
[25] purrr_0.3.5 ellipsis_0.3.2
[27] backports_1.4.1 V8_4.2.1
[29] insight_0.18.6 MatrixGenerics_1.8.1
[31] vctrs_0.5.0 Biobase_2.56.0
[33] sjlabelled_1.2.0 abind_1.4-5
[35] cachem_1.0.6 withr_2.5.0
[37] robustbase_0.95-0 rgdal_1.5-32
[39] emmeans_1.8.2 getopt_1.20.3
[41] svglite_2.1.0 lazyeval_0.2.2
[43] crayon_1.5.2 flexdashboard_0.6.0
[45] pkgconfig_2.0.3 labeling_0.4.2
[47] rlang_1.0.6 lifecycle_1.0.3
[49] miniUI_0.1.1.1 modelr_0.1.9
[51] cellranger_1.1.0 datawizard_0.6.3
[53] raster_3.6-3 carData_3.0-5
[55] lpsymphony_1.24.0 Rhdf5lib_1.18.2
[57] boot_1.3-28 viridisLite_0.4.1
[59] parameters_0.19.0 rootSolve_1.8.2.3
[61] bitops_1.0-7 rhdf5filters_1.8.0
[63] blob_1.2.3 stringr_1.4.1
[65] rstatix_0.7.0 memoise_2.0.1
[67] zlibbioc_1.42.0 compiler_4.2.1
[69] cli_3.4.1 ade4_1.7-19
[71] tidyselect_1.2.0 stringi_1.7.8
[73] highr_0.9 yaml_2.3.6
[75] grid_4.2.1 sass_0.4.2
[77] fastmatch_1.1-3 tools_4.2.1
[79] lmom_2.9 rstudioapi_0.14
[81] foreach_1.5.2 optparse_1.7.3
[83] gld_2.6.6 farver_2.1.1
[85] Rtsne_0.16 RcppZiggurat_0.1.6
[87] digest_0.6.30 quadprog_1.5-8
[89] Rcpp_1.0.9 GenomicRanges_1.48.0
[91] car_3.1-1 broom_1.0.1
[93] performance_0.10.0 later_1.3.0
[95] httr_1.4.4 effectsize_0.8.1
[97] colorspace_2.0-3 rvest_1.0.3
[99] splines_4.2.1 expm_0.999-6
[101] sp_1.5-0 multtest_2.52.0
[103] Exact_3.2 systemfonts_1.0.4
[105] xtable_1.8-4 jsonlite_1.8.3
[107] nloptr_2.0.3 Rfast_2.0.6
[109] R6_2.5.1 pillar_1.8.1
[111] htmltools_0.5.3 mime_0.12
[113] glue_1.6.2 fastmap_1.1.0
[115] minqa_1.2.5 BiocParallel_1.30.4
[117] class_7.3-20 codetools_0.2-18
[119] pcaPP_2.0-3 mvtnorm_1.1-3
[121] utf8_1.2.2 bslib_0.4.0
[123] tibble_3.1.8 curl_4.3.3
[125] biglm_0.9-2.1 rmarkdown_2.17
[127] biomformat_1.24.0 munsell_0.5.0
[129] e1071_1.7-12 rhdf5_2.40.0
[131] GenomeInfoDbData_1.2.8 iterators_1.0.14
[133] sjmisc_2.8.9 gtable_0.3.1
[135] bayestestR_0.13.0 .